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Title: The potato NB LRR gene family : determination, characterisation and utilisation for rapid identification of novel disease resistance genes
Author: Jupe, Florian
Awarding Body: University of East Anglia
Current Institution: University of East Anglia
Date of Award: 2012
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The potato genome sequence derived from a double-monoploid Solanum tuberosum Group Phureja clone provides unparalleled insight into the genome composition of this important crop, including its repertoire of disease resistance genes. The vast majority of plant resistance (R) genes contain a nucleotide-binding and leucine-rich repeat domain, and are collectively known as NB-LRRs. The aim of this thesis is to aid the annotation of this gene family in potato and to use this information to accelerate the process of functional R gene isolation. The first part of this Thesis reports the identification and phylogenetic characterisation of 438 NB-LRR genes through an amino-acid motif based search of the 39,000 potato gene models. A full re-annotation of the singe sequences provided a blueprint for a sequence capture approach to enrich for NB-LRR specific sequences prior next-generation sequencing, as reported in the second part of this thesis. In a poof-of-concept study that was carried out on the sequenced potato clone, not only 424 of the previously identified genes were verified, but further 338 NB-LRR encoding sequences were identified, mainly from un-annotated regions of the genome. Physical map positions were established for 83% of the predicted NB-LRRs across all we potato chromosomes. The third part of this thesis reports on the characterisation of the genetic basis of the late blight resistance of the potato cultivar Sarpo Mira. Whole plant assays with two aggressive late blight isolates identified a differential segregation for resistance within a population derived from a cross with the susceptible cultivar Maris Piper. Transient expression of characterised late blight effector genes gave evidence for a novel resistance gene composition with Sarpo Mira. A sequencing based genotyping approach identified five loci on chromosomes 5, 11 and 12 with positive impact on the resistance. Analysis of NB-LRR enriched illumina reads of bulked resistant and susceptible plants was however inconclusive, due to difficulties arising from the tetraploid genetic background of Sarpo Mira.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available